PGAdb-builder in pipeline

[…] (huson, ). the equal angle method was used to construct the phylogenetic network, which was plotted with neighbornet., a wgmlst analysis was performed using the build_wgmlsttree module in the pgadb-builder web service tool (liu et al., ). the 17 genome sequences were compared with the resulting pgadb profile using blastn, with filters of 80% coverage and 90% identity., we also performed […]

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[…] (huson, ). the equal angle method was used to construct the phylogenetic network, which was plotted with neighbornet., a wgmlst analysis was performed using the build_wgmlsttree module in the pgadb-builder web service tool (liu et al., ). the 17 genome sequences were compared with the resulting pgadb profile using blastn, with filters of 80% coverage and 90% identity., we also performed […]

[…] to refine their evolutionary relationships which unfortunately is beyond the scope of this study. such wgmlst analysis can be performed using existing bioinformatic tools such as bigsdb, roary and pgadb-builder (jolley and maiden, ; page et al., ; liu et al., ). strikingly, several whole genome sequences labeled as the same pseudomonas species were located in different major clades […]

[…] complete genomic sequences or genomic contigs were first annotated using prokka (), a rapid bacterial genome annotation pipeline, to generate output gff files. the gff files were processed using the pgadb_builder, a pipeline for construction of a bacterial pan-genome allele database (). in this study, paralogous genes were excluded from the dataset, and proteins sharing ≥95% amino acid sequence […]

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Supported by grant from ‘Academic Summit Program’ of Ministry of Science and Technology (MOST-105-2221-E-110-079), ‘Medical Science and Technology Center of Aiming for the Top University Program’ of National Sun Yat-sen University and Ministry of Education, Taiwan, and also a grant (MOHW105- CDC-C-315-123301) from Centers for Disease Control, the Ministry of Health and Welfare, Taiwan.

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